Package picard

Examples of picard.PicardException

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    final File PLOTS_OUT = new File(METRICS_FILE_PREFIX + PDF_FILE_EXTENSION);
    assertIoFiles(SUMMARY_OUT, DETAILS_OUT, PLOTS_OUT);

    final SAMFileReader samReader = new SAMFileReader(INPUT);
    if (!ASSUME_SORTED && samReader.getFileHeader().getSortOrder() != SAMFileHeader.SortOrder.coordinate) {
      throw new PicardException("The input file " + INPUT.getAbsolutePath() + " does not appear to be coordinate sorted");
    }

    final ReferenceSequenceFileWalker refWalker = new ReferenceSequenceFileWalker(REFERENCE);
    final ProgressLogger progressLogger = new ProgressLogger(log);
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    /**
     * Return a regex string for finding Lane and Tile given a file extension pattern
     */
    public static String makeLaneTileRegex(final String fileNameEndPattern, final int lane) {
        if (lane < 0) {
            throw new PicardException("Lane (" + lane + ") cannot be negative");
        }
        return "^" + "s_" + lane + "_(\\d{1,5})" + fileNameEndPattern + "$";
    }
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            // Get a mapping from metric code number to the corresponding IlluminaTileMetrics
            final Map<Integer, Collection<IlluminaTileMetrics>> codeMetricsMap = partitionTileMetricsByCode(tileRecords);

            final Set<Integer> observedCodes = codeMetricsMap.keySet();
            if (!(observedCodes.contains(IlluminaMetricsCode.DENSITY_ID.getMetricsCode()) && observedCodes.contains(IlluminaMetricsCode.CLUSTER_ID.getMetricsCode())))
                throw new PicardException(String.format("Expected to find cluster and density record codes (%s and %s) in records read for tile location %s (lane:tile), but found only %s.",
                        IlluminaMetricsCode.CLUSTER_ID.getMetricsCode(), IlluminaMetricsCode.DENSITY_ID.getMetricsCode(), entry.getKey(), observedCodes));

            final IlluminaTileMetrics densityRecord = CollectionUtil.getSoleElement(codeMetricsMap.get(IlluminaMetricsCode.DENSITY_ID.getMetricsCode()));
            final IlluminaTileMetrics clusterRecord = CollectionUtil.getSoleElement(codeMetricsMap.get(IlluminaMetricsCode.CLUSTER_ID.getMetricsCode()));
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                // For both phasing & prephasing, pull out the value and create a TilePhasingValue for further processing
                final int phasingCode = IlluminaMetricsCode.getPhasingCode(descriptorIndex, IlluminaMetricsCode.PHASING_BASE);
                final int prePhasingCode = IlluminaMetricsCode.getPhasingCode(descriptorIndex, IlluminaMetricsCode.PREPHASING_BASE);

                if (!(codeMetricsMap.containsKey(phasingCode) && codeMetricsMap.containsKey(prePhasingCode))) {
                    throw new PicardException("Don't have both phasing and prephasing values for tile");
                }

                tilePhasingValues.add(new TilePhasingValue(tileTemplateRead,
                        CollectionUtil.getSoleElement(codeMetricsMap.get(phasingCode)).getMetricValue(),
                        CollectionUtil.getSoleElement(codeMetricsMap.get(prePhasingCode)).getMetricValue()));
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            case Clocs:
                fileReader = new ClocsFileReader(file);
                break;

            default:
                throw new PicardException("Unrecognized pos file type " + fileType.name());
        }

        return new CloseableIterator<PositionalData>() {
            private AbstractIlluminaPositionFileReader reader = fileReader;
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            case C: return c;
            case G: return g;
            case T: return t;
        }

        throw new PicardException("Unexpected intensity channel " + channel);
    }
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            this.out.writeShort(read.tile);
            this.out.writeShort(read.x);
            this.out.writeShort(read.y);
            this.out.writeByte(read.orientationForOpticalDuplicates);
        } catch (final IOException ioe) {
            throw new PicardException("Exception writing ReadEnds to file.", ioe);
        }
    }
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            read.orientationForOpticalDuplicates = this.in.readByte();

            return read;
        } catch (final IOException ioe) {
            throw new PicardException("Exception writing ReadEnds to file.", ioe);
        }
    }
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        for (final File f : INPUT) {
            final SAMFileReader reader = new SAMFileReader(f, true); // eager decode
            final SAMFileHeader header = reader.getFileHeader();

            if (!ASSUME_SORTED && header.getSortOrder() != SAMFileHeader.SortOrder.coordinate) {
                throw new PicardException("Input file " + f.getAbsolutePath() + " is not coordinate sorted.");
            }

            headers.add(header);
            readers.add(reader);
        }
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                    OUTPUT.getAbsolutePath(),
                    CHART_OUTPUT.getAbsolutePath(),
                    INPUT.getName(),
                    plotSubtitle);
            if (rResult != 0) {
                throw new PicardException("R script nucleotideDistributionByCycle.R failed with return code " + rResult);
            }
        }
    }
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Related Classes of picard.PicardException

  • picard.analysis.directed.RnaSeqMetricsCollector
  • picard.cmdline.CommandLineParser
  • picard.fastq.BamToBfqWriter
  • picard.illumina.CheckIlluminaDirectory
  • picard.illumina.IlluminaBasecallsConverter
  • picard.illumina.IlluminaBasecallsToFastq
  • picard.illumina.IlluminaBasecallsToSam
  • picard.illumina.parser.ClusterData
  • picard.illumina.parser.ClusterIntensityFileReader
  • picard.illumina.parser.IlluminaDataProvider
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